blast_encoding.h

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_encoding.h,v $
 * PRODUCTION Revision 1000.0  2004/04/12 17:53:18  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_CORE___BLAST_ENCODING__H
#define ALGO_BLAST_CORE___BLAST_ENCODING__H

/*  $Id: blast_encoding.h,v 1000.0 2004/04/12 17:53:18 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Christiam Camacho
 *
 */

/** @file blast_encoding.h
 *  Declarations of static arrays used to define some NCBI encodings to be used
 *  in a toolkit independent manner by the BLAST engine.
 */

#include <algo/blast/core/ncbi_std.h>

/** @addtogroup AlgoBlast
 *
 * @{
 */

#ifdef __cplusplus
extern "C" {
#endif

/* Nucleotide encodings */

/** Translates between ncbi4na and blastna. The first four elements
 *	of this array match ncbi2na. */
extern const Uint1 NCBI4NA_TO_BLASTNA[];

/** Translates between blastna and ncbi4na. */
extern const Uint1 BLASTNA_TO_NCBI4NA[];

/** Translates between iupacna and blastna. */
extern const Uint1 IUPACNA_TO_BLASTNA[];

/** Translates between iupacna and ncbi4na. */
extern const Uint1 IUPACNA_TO_NCBI4NA[];

/** Translates between ncbieaa and ncbistdaa. */
extern const Uint1 AMINOACID_TO_NCBISTDAA[];

#define BLASTNA_SIZE 16     /**< Size of nucleic acid alphabet */
#define BLASTAA_SIZE 26     /**< Size of aminoacid alphabet */

/* Identifies the blastna alphabet, for use in blast only. */
#define BLASTNA_SEQ_CODE 99
#define BLASTAA_SEQ_CODE 11 /**< == Seq_code_ncbistdaa */
#define NCBI4NA_SEQ_CODE 4  /**< == Seq_code_ncbi4na */	

/** @bug FIXME: Should this be removed since it's the same as BLASTAA_SIZE ? */
#define PSI_ALPHABET_SIZE  26

#ifdef __cplusplus
}
#endif

/* @} */


/*
 * ===========================================================================
 * $Log: blast_encoding.h,v $
 * Revision 1000.0  2004/04/12 17:53:18  gouriano
 * PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.3
 *
 * Revision 1.3  2004/04/09 14:48:05  camacho
 * Added doxygen comments
 *
 * Revision 1.2  2004/04/07 19:05:44  camacho
 * Minor fix in #ifdef guards
 *
 * Revision 1.1  2004/04/07 03:10:20  camacho
 * Initial revision
 *
 * ===========================================================================
 */

#endif  /* ALGO_BLAST_CORE___BLAST_ENCODING__H */